MolNFT v1 · #81217 · protein
Crystal structure of the TIP48 (TIP49B) hexamer
3UK6 · Ruvb-like 2: “Crystal structure of the TIP48 (TIP49B) hexamer”. X-ray diffraction, 1 ligand (ADP), 20 pockets (best druggability 0.83). MolNFT v1 #81217 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3UK6
- Type
- protein
- Length
- 3,526 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ruvb-like 2
- EC
- 3.6.4.12
- UniProt
- Q9Y230
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 12 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ruvb-like 2 (EC 3.6.4.12) | protein | 298 | 49% helix, 17% strand | Q9Y230 |
| B | Ruvb-like 2 (EC 3.6.4.12) | protein | 300 | 48% helix, 18% strand | Q9Y230 |
| C | Ruvb-like 2 (EC 3.6.4.12) | protein | 321 | 46% helix, 17% strand | Q9Y230 |
| D | Ruvb-like 2 (EC 3.6.4.12) | protein | 299 | 47% helix, 16% strand | Q9Y230 |
| E | Ruvb-like 2 (EC 3.6.4.12) | protein | 290 | 48% helix, 16% strand | Q9Y230 |
| F | Ruvb-like 2 (EC 3.6.4.12) | protein | 301 | 47% helix, 18% strand | Q9Y230 |
| G | Ruvb-like 2 (EC 3.6.4.12) | protein | 330 | 45% helix, 17% strand | Q9Y230 |
| H | Ruvb-like 2 (EC 3.6.4.12) | protein | 277 | 50% helix, 17% strand | Q9Y230 |
| I | Ruvb-like 2 (EC 3.6.4.12) | protein | 294 | 49% helix, 15% strand | Q9Y230 |
| J | Ruvb-like 2 (EC 3.6.4.12) | protein | 300 | 45% helix, 17% strand | Q9Y230 |
| K | Ruvb-like 2 (EC 3.6.4.12) | protein | 283 | 48% helix, 16% strand | Q9Y230 |
| L | Ruvb-like 2 (EC 3.6.4.12) | protein | 233 | 50% helix, 16% strand | Q9Y230 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1123 | 0.83 | 0.84 | 117 | ADP |
| 2 | 1183 | 0.82 | 0.83 | 119 | ADP |
| 3 | 1041 | 0.81 | 0.82 | 118 | ADP |
| 4 | 958 | 0.78 | 0.80 | 111 | ADP |
| 5 | 903 | 0.78 | 0.80 | 108 | ADP |
Interfaces
13 interfaces between chains.
- F–G · 1802 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1645 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 1632 Ų buried · 4 hydrogen bonds · protein-protein
- D–I · 1575 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1532 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3UK6 · Crystal Structure of the Tip48 (Tip49b) hexamer · the same entry in another collection · chain L against L, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9Y230
- Elsewhere: RCSB PDB 3UK6 · PDBe 3UK6 · UniProt Q9Y230
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